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Omotesho QA, Escamilla A, Pérez-Ruiz E, Frecha CA, Rueda-Domínguez A, Barragán I. Epigenetic targets to enhance antitumor immune response through the induction of tertiary lymphoid structures. Front Immunol 2024; 15:1348156. [PMID: 38333212 PMCID: PMC10851080 DOI: 10.3389/fimmu.2024.1348156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024] Open
Abstract
Tertiary lymphoid structures (TLS) are ectopic lymphoid aggregates found in sites of chronic inflammation such as tumors and autoimmune diseases. The discovery that TLS formation at tumor sites correlated with good patient prognosis has triggered extensive research into various techniques to induce their formation at the tumor microenvironment (TME). One strategy is the exogenous induction of specific cytokines and chemokine expression in murine models. However, applying such systemic chemokine expression can result in significant toxicity and damage to healthy tissues. Also, the TLS formed from exogenous chemokine induction is heterogeneous and different from the ones associated with favorable prognosis. Therefore, there is a need to optimize additional approaches like immune cell engineering with lentiviral transduction to improve the TLS formation in vivo. Similarly, the genetic and epigenetic regulation of the different phases of TLS neogenesis are still unknown. Understanding these molecular regulations could help identify novel targets to induce tissue-specific TLS in the TME. This review offers a unique insight into the molecular checkpoints of the different stages and mechanisms involved in TLS formation. This review also highlights potential epigenetic targets to induce TLS neogenesis. The review further explores epigenetic therapies (epi-therapy) and ongoing clinical trials using epi-therapy in cancers. In addition, it builds upon the current knowledge of tools to generate TLS and TLS phenotyping biomarkers with predictive and prognostic clinical potential.
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Affiliation(s)
- Quadri Ajibola Omotesho
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy and Epigenetics), Regional and Clinical University Hospitals, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Malaga, Spain
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Alejandro Escamilla
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy and Epigenetics), Regional and Clinical University Hospitals, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Malaga, Spain
- Department of Human Physiology, Human Histology, Pathological Anatomy and Physical Sport Education, University of Malaga, Malaga, Spain
| | - Elisabeth Pérez-Ruiz
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy and Epigenetics), Regional and Clinical University Hospitals, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Malaga, Spain
| | - Cecilia A. Frecha
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Civil Hospital, Malaga, Spain
| | - Antonio Rueda-Domínguez
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy and Epigenetics), Regional and Clinical University Hospitals, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Malaga, Spain
| | - Isabel Barragán
- Medical Oncology Service (Group of Translational Research in Cancer Immunotherapy and Epigenetics), Regional and Clinical University Hospitals, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Malaga, Spain
- Group of Pharmacoepigenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
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2
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Hu Y, Guo H, He L, Wang Q, Li Y, Weng J, Zhang R. The Correlation Between IFNG Gene Methylation and Th1|Th2 Cell Balance in ROU and the Interventional Study of Jiaweidaochi Powder. Appl Biochem Biotechnol 2023; 195:6737-6751. [PMID: 36917437 DOI: 10.1007/s12010-023-04417-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/16/2023]
Abstract
The pathogenesis of recurrent oral ulcers (ROU) is complex, with a long duration of illness and challenging to cure. According to traditional Chinese medicine (TCM),"heat accumulation in the heart-spleen" is one of the main causative factors. Jiaweidaochi powder (JWDCP) is based on the ancient Chinese medicine formula JWDCS, with the addition of Tongcao and gypsum and the removal of Mu Tong. It is generally used to treat "heat accumulation in the heart-spleen." Previous studies have demonstrated that it effectively reduces recurrence rates and is anti-inflammatory in modulating immunity. The ROU rats' model for JWDCP intervention treatment had been established, and histological tests revealed that JWDCP has a therapeutic effect on the pathological changes in the oral mucosa. In addition, the methylation levels of peripheral blood IFNG gene were detected by bisulfite sequencing PCR (BSP), and the methylation levels of the IFNG promoter region in the model group and each dose group were lower than those in the control group. However, no significant methylation differences were observed. Furthermore, the results of enzyme-linked immunosorbent assay (ELISA) and RNA quantitative polymerase chain reaction showed that JWDCP could reduce IFN-γ and IL-4 protein concentrations, with high GATA-3 mRNA production, T-bet mRNAproduction was upgraded, elevated IL-4 mRNA levels, and reduced IFN-γ mRNA levels after treatment (P < 0.001). The expression of transcription factor T-betmRNA and GATA-3 gene mRNA was accompanied by changes in IFN-γmRNA and IL-4mRNA, demonstrating that Th2 type differentiation in RAS suppresses the body's immunity and that the imbalance of transcription factor expression further leads to Th1/Th2 drift. JWDCP is likely to reduce the protein concentration by regulating the imbalance of transcription factors and enhancing antioxidant capacity, thus achieving therapeutic effects. Treatment of recurrent oral ulcer models is not sufficient to reset IFNG methylation levels, correlating with the refractoriness of ROU, further confirming the complexity of epigenetic mechanisms and that epigenetic alterations in specific mediators may persist locally.
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Affiliation(s)
- Yue Hu
- Department of Graduate School, Shanxi University of Chinese Medicine, Taiyuan, 030619, China
| | - Hongbo Guo
- Department of Traditional Chinese Medicine, First Hospital of Shanxi Medical University, Taiyuan, 030001, China.
| | - Lu He
- Department of Traditional Chinese Medicine, Xingyi People's Hospital, Xingyi, 562400, China
| | - Qianqian Wang
- Department of Graduate School, Shanxi Medical University, Taiyuan, 030001, China
| | - Yanqing Li
- Department of Graduate School, Shanxi Medical University, Taiyuan, 030001, China
| | - Jiankun Weng
- Department of Graduate School, Shanxi University of Chinese Medicine, Taiyuan, 030619, China
| | - Rong Zhang
- Department of Graduate School, Shanxi Medical University, Taiyuan, 030001, China
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3
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Lin J, Liu J, Ma R, Hao J, Liang Y, Zhao J, Zhang A, Meng H, Lu J. Interleukin-33: Metabolic checkpoints, metabolic processes, and epigenetic regulation in immune cells. Front Immunol 2022; 13:900826. [PMID: 35979357 PMCID: PMC9376228 DOI: 10.3389/fimmu.2022.900826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Interleukin-33 (IL-33) is a pleiotropic cytokine linked to various immune cells in the innate and adaptive immune systems. Recent studies of the effects of IL-33 on immune cells are beginning to reveal its regulatory mechanisms at the levels of cellular metabolism and epigenetic modifications. In response to IL-33 stimulation, these programs are intertwined with transcriptional programs, ultimately determining the fate of immune cells. Understanding these specific molecular events will help to explain the complex role of IL-33 in immune cells, thereby guiding the development of new strategies for immune intervention. Here, we highlight recent findings that reveal how IL-33, acting as an intracellular nuclear factor or an extracellular cytokine, alters metabolic checkpoints and cellular metabolism, which coordinately contribute to cell growth and function. We also discuss recent studies supporting the role of IL-33 in epigenetic alterations and speculate about the mechanisms underlying this relationship.
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Affiliation(s)
- Jian Lin
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiyun Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Rui Ma
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Hao
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Liang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junjie Zhao
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ailing Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haiyang Meng
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingli Lu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Jingli Lu,
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4
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Hertweck A, Vila de Mucha M, Barber PR, Dagil R, Porter H, Ramos A, Lord GM, Jenner RG. The TH1 cell lineage-determining transcription factor T-bet suppresses TH2 gene expression by redistributing GATA3 away from TH2 genes. Nucleic Acids Res 2022; 50:4557-4573. [PMID: 35438764 PMCID: PMC9071441 DOI: 10.1093/nar/gkac258] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 03/28/2022] [Accepted: 04/13/2022] [Indexed: 11/12/2022] Open
Abstract
Lineage-determining transcription factors (LD-TFs) drive the differentiation of progenitor cells into a specific lineage. In CD4+ T cells, T-bet dictates differentiation of the TH1 lineage, whereas GATA3 drives differentiation of the alternative TH2 lineage. However, LD-TFs, including T-bet and GATA3, are frequently co-expressed but how this affects LD-TF function is not known. By expressing T-bet and GATA3 separately or together in mouse T cells, we show that T-bet sequesters GATA3 at its target sites, thereby removing GATA3 from TH2 genes. This redistribution of GATA3 is independent of GATA3 DNA binding activity and is instead mediated by the T-bet DNA binding domain, which interacts with the GATA3 DNA binding domain and changes GATA3's sequence binding preference. This mechanism allows T-bet to drive the TH1 gene expression program in the presence of GATA3. We propose that redistribution of one LD-TF by another may be a common mechanism that could explain how specific cell fate choices can be made even in the presence of other transcription factors driving alternative differentiation pathways.
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Affiliation(s)
- Arnulf Hertweck
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
| | - Maria Vila de Mucha
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
| | - Paul R Barber
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK.,Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, King's College London, London, SE1 1UL, UK
| | - Robert Dagil
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK
| | - Hayley Porter
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
| | - Andres Ramos
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK
| | - Graham M Lord
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9NT, UK
| | - Richard G Jenner
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
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5
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Kania AK, Price MJ, George-Alexander LE, Patterson DG, Hicks SL, Scharer CD, Boss JM. H3K27me3 Demethylase UTX Restrains Plasma Cell Formation. THE JOURNAL OF IMMUNOLOGY 2022; 208:1873-1885. [PMID: 35346967 PMCID: PMC9012698 DOI: 10.4049/jimmunol.2100948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/02/2022] [Indexed: 11/19/2022]
Abstract
B cell differentiation is associated with substantial transcriptional, metabolic, and epigenetic remodeling, including redistribution of histone 3 lysine 27 trimethylation (H3K27me3), which is associated with a repressive chromatin state and gene silencing. Although the role of the methyltransferase EZH2 (Enhancer of zeste homolog 2) in B cell fate decisions has been well established, it is not known whether H3K27me3 demethylation is equally important. In this study, we showed that simultaneous genetic deletion of the two H3K27 demethylases UTX and JMJD3 (double-knockout [Utx fl/fl Jmjd3 fl/fl Cd19 cre/+] [dKO]) led to a significant increase in plasma cell (PC) formation after stimulation with the T cell-independent Ags LPS and NP-Ficoll. This phenotype occurred in a UTX-dependent manner as UTX single-knockout mice, but not JMJD3 single-knockout mice, mimicked the dKO. Although UTX- and JMJD3-deficient marginal zone B cells showed increased proliferation, dKO follicular B cells also showed increased PC formation. PCs from dKO mice upregulated genes associated with oxidative phosphorylation and exhibited increased spare respiratory capacity. Mechanistically, deletion of Utx and Jmjd3 resulted in higher levels of H3K27me3 at proapoptotic genes and resulted in reduced apoptosis of dKO PCs in vivo. Furthermore, UTX regulated chromatin accessibility at regions containing ETS and IFN regulatory factor (IRF) transcription factor family motifs, including motifs of known repressors of PC fate. Taken together, these data demonstrate that the H3K27me3 demethylases restrain B cell differentiation.
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Affiliation(s)
- Anna K Kania
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Madeline J Price
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | | | - Dillon G Patterson
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Sakeenah L Hicks
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
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6
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Henderson S, Pullabhatla V, Hertweck A, de Rinaldis E, Herrero J, Lord GM, Jenner RG. The Th1 cell regulatory circuitry is largely conserved between human and mouse. Life Sci Alliance 2021; 4:4/11/e202101075. [PMID: 34531288 PMCID: PMC8960437 DOI: 10.26508/lsa.202101075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 12/24/2022] Open
Abstract
Comparison of the binding sites of the Th1 lineage-specifying transcription factor T-bet between human and mouse reveals differences in binding sites but that the most of the target genes are shared. Gene expression programs controlled by lineage-determining transcription factors are often conserved between species. However, infectious diseases have exerted profound evolutionary pressure, and therefore the genes regulated by immune-specific transcription factors might be expected to exhibit greater divergence. T-bet (Tbx21) is the immune-specific, lineage-specifying transcription factor for T helper type I (Th1) immunity, which is fundamental for the immune response to intracellular pathogens but also underlies inflammatory diseases. We compared T-bet genomic targets between mouse and human CD4+ T cells and correlated T-bet binding patterns with species-specific gene expression. Remarkably, we found that the majority of T-bet target genes are conserved between mouse and human, either via preservation of binding sites or via alternative binding sites associated with transposon-linked insertion. Species-specific T-bet binding was associated with differences in transcription factor–binding motifs and species-specific expression of associated genes. These results provide a genome-wide cross-species comparison of Th1 gene regulation that will enable more accurate translation of genetic targets and therapeutics from pre-clinical models of inflammatory and infectious diseases and cancer into human clinical trials.
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Affiliation(s)
- Stephen Henderson
- Bill Lyons Informatics Centre, UCL Cancer Institute and CRUK UCL Centre, University College London, London, UK
| | - Venu Pullabhatla
- NIHR Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, UK
| | - Arnulf Hertweck
- Regulatory Genomics Group, UCL Cancer Institute and CRUK UCL Centre, University College London, London, UK
| | - Emanuele de Rinaldis
- NIHR Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, UK
| | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute and CRUK UCL Centre, University College London, London, UK
| | - Graham M Lord
- NIHR Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, UK .,School of Immunology and Microbial Sciences, King's College London, London, UK.,Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Richard G Jenner
- Regulatory Genomics Group, UCL Cancer Institute and CRUK UCL Centre, University College London, London, UK
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7
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Solé P, Santamaria P. Re-Programming Autoreactive T Cells Into T-Regulatory Type 1 Cells for the Treatment of Autoimmunity. Front Immunol 2021; 12:684240. [PMID: 34335585 PMCID: PMC8320845 DOI: 10.3389/fimmu.2021.684240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
Systemic delivery of peptide-major histocompatibility complex (pMHC) class II-based nanomedicines can re-program cognate autoantigen-experienced CD4+ T cells into disease-suppressing T-regulatory type 1 (TR1)-like cells. In turn, these TR1-like cells trigger the formation of complex regulatory cell networks that can effectively suppress organ-specific autoimmunity without impairing normal immunity. In this review, we summarize our current understanding of the transcriptional, phenotypic and functional make up of TR1-like cells as described in the literature. The true identity and direct precursors of these cells remain unclear, in particular whether TR1-like cells comprise a single terminally-differentiated lymphocyte population with distinct transcriptional and epigenetic features, or a collection of phenotypically different subsets sharing key regulatory properties. We propose that detailed transcriptional and epigenetic characterization of homogeneous pools of TR1-like cells will unravel this conundrum.
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Affiliation(s)
- Patricia Solé
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Pere Santamaria
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain.,Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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8
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Wu Y, Jin X, Zhang Y, Zheng J, Yang R. Genetic and epigenetic mechanisms in the development of congenital heart diseases. WORLD JOURNAL OF PEDIATRIC SURGERY 2021; 4:e000196. [DOI: 10.1136/wjps-2020-000196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Congenital heart disease (CHD) is the most common of congenital cardiovascular malformations associated with birth defects, and it results in significant morbidity and mortality worldwide. The classification of CHD is still elusive owing to the complex pathogenesis of CHD. Advances in molecular medicine have revealed the genetic basis of some heart anomalies. Genes associated with CHD might be modulated by various epigenetic factors. Thus, the genetic and epigenetic factors are gradually accepted as important triggers in the pathogenesis of CHD. However, few literatures have comprehensively elaborated the genetic and epigenetic mechanisms of CHD. This review focuses on the etiology of CHD from genetics and epigenetics to discuss the role of these factors in the development of CHD. The interactions between genetic and epigenetic in the pathogenesis of CHD are also elaborated. Chromosome abnormalities and gene mutations in genetics, and DNA methylations, histone modifications and on-coding RNAs in epigenetics are summarized in detail. We hope the summative knowledge of these etiologies may be useful for improved diagnosis and further elucidation of CHD so that morbidity and mortality of children with CHD can be reduced in the near future.
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9
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Li J, Hardy K, Olshansky M, Barugahare A, Gearing LJ, Prier JE, Sng XYX, Nguyen MLT, Piovesan D, Russ BE, La Gruta NL, Hertzog PJ, Rao S, Turner SJ. KDM6B-dependent chromatin remodeling underpins effective virus-specific CD8 + T cell differentiation. Cell Rep 2021; 34:108839. [PMID: 33730567 DOI: 10.1016/j.celrep.2021.108839] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 11/24/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Naive CD8+ T cell activation results in an autonomous program of cellular proliferation and differentiation. However, the mechanisms that underpin this process are unclear. Here, we profile genome-wide changes in chromatin accessibility, gene transcription, and the deposition of a key chromatin modification (H3K27me3) early after naive CD8+ T cell activation. Rapid upregulation of the histone demethylase KDM6B prior to the first cell division is required for initiating H3K27me3 removal at genes essential for subsequent T cell differentiation and proliferation. Inhibition of KDM6B-dependent H3K27me3 demethylation limits the magnitude of an effective primary virus-specific CD8+ T cell response and the formation of memory CD8+ T cell populations. Accordingly, we define the early spatiotemporal events underpinning early lineage-specific chromatin reprogramming that are necessary for autonomous CD8+ T cell proliferation and differentiation.
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Affiliation(s)
- Jasmine Li
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kristine Hardy
- Epigenetics and Transcription Laboratory Melanie Swan Memorial Translational Centre, Sci-Tech, University of Canberra, Bruce, ACT 2617, Australia
| | - Moshe Olshansky
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Adele Barugahare
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Linden J Gearing
- Hudson Institute for Medical Research, Clayton, VIC 3168, Australia
| | - Julia E Prier
- Department of Microbiology and Immunology, the Doherty Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Xavier Y X Sng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Michelle Ly Thai Nguyen
- Department of Microbiology and Immunology, the Doherty Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Dana Piovesan
- Department of Microbiology and Immunology, the Doherty Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Brendan E Russ
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Nicole L La Gruta
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Paul J Hertzog
- Hudson Institute for Medical Research, Clayton, VIC 3168, Australia
| | - Sudha Rao
- QIMR Berghofer Gene Regulation and Translational Medicine Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Stephen J Turner
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Hudson Institute for Medical Research, Clayton, VIC 3168, Australia.
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10
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Clark M, Kroger CJ, Ke Q, Tisch RM. The Role of T Cell Receptor Signaling in the Development of Type 1 Diabetes. Front Immunol 2021; 11:615371. [PMID: 33603744 PMCID: PMC7884625 DOI: 10.3389/fimmu.2020.615371] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022] Open
Abstract
T cell receptor (TCR) signaling influences multiple aspects of CD4+ and CD8+ T cell immunobiology including thymic development, peripheral homeostasis, effector subset differentiation/function, and memory formation. Additional T cell signaling cues triggered by co-stimulatory molecules and cytokines also affect TCR signaling duration, as well as accessory pathways that further shape a T cell response. Type 1 diabetes (T1D) is a T cell-driven autoimmune disease targeting the insulin producing β cells in the pancreas. Evidence indicates that dysregulated TCR signaling events in T1D impact the efficacy of central and peripheral tolerance-inducing mechanisms. In this review, we will discuss how the strength and nature of TCR signaling events influence the development of self-reactive T cells and drive the progression of T1D through effects on T cell gene expression, lineage commitment, and maintenance of pathogenic anti-self T cell effector function.
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Affiliation(s)
- Matthew Clark
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Charles J Kroger
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Qi Ke
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Roland M Tisch
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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11
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Spinner CA, Lazarevic V. Transcriptional regulation of adaptive and innate lymphoid lineage specification. Immunol Rev 2020; 300:65-81. [PMID: 33615514 DOI: 10.1111/imr.12935] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/26/2020] [Accepted: 11/16/2020] [Indexed: 12/28/2022]
Abstract
Once alerted to the presence of a pathogen, activated CD4+ T cells initiate distinct gene expression programs that produce multiple functionally specialized T helper (Th) subsets. The cytokine milieu present at the time of antigen encounter instructs CD4+ T cells to differentiate into interferon-(IFN)-γ-producing Th1 cells, interleukin-(IL)-4-producing Th2 cells, IL-17-producing Th17 cells, follicular T helper (Tfh) cells, or regulatory T (Treg) cells. In each of these Th cell subsets, a single transcription factor has been identified as a critical regulator of its specialized differentiation program. In this context, the expression of the "master regulator" is necessary and sufficient to activate lineage-specific genes while restricting the gene expression program of alternative Th fates. Thus, the transcription factor T-bet controls Th1 differentiation program, while the development of Th2, Th17, Tfh, and Treg cells is dependent on transcription factors GATA3, RORγt, Bcl6, and Foxp3, respectively. Nevertheless, master regulators or, more precisely, lineage-defining transcription factors do not function in isolation. In fact, they interact with a complex network of transcription factors, orchestrating cell lineage specification programs. In this review, we discuss the concept of the combinatorial interactions of key transcription factors in determining helper T cell identity. Additionally, lineage-defining transcription factors have well-established functions beyond their role in CD4+ Th subsets. They play critically important functions at distinct stages during T cell development in the thymus and they control the development of innate lymphoid cells (ILCs) in the bone marrow. In tracking the journey of T cells traversing from the thymus to the periphery and during the immune response, we discuss in broad terms developmental stage and context-dependent functions of lineage-defining transcription factors in regulating specification programs of innate and adaptive lymphocytes.
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Affiliation(s)
- Camille A Spinner
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vanja Lazarevic
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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12
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Wehn AK, Farkas DR, Sedlock CE, Subedi D, Chapman DL. Functionally distinct roles for T and Tbx6 during mouse development. Biol Open 2020; 9:9/8/bio054692. [PMID: 32855167 PMCID: PMC7473639 DOI: 10.1242/bio.054692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mouse T-box transcription factors T and Tbx6 are co-expressed in the primitive streak and have unique domains of expression; T is expressed in the notochord, while Tbx6 is expressed in the presomitic mesoderm. T-box factors are related through a shared DNA binding domain, the T-domain, and can therefore bind to similar DNA sequences at least in vitro. We investigated the functional similarities and differences of T and Tbx6 DNA binding and transcriptional activity in vitro and their interaction genetically in vivo. We show that at one target, Dll1, the T-domains of T and Tbx6 have different affinities for the binding sites present in the mesoderm enhancer. We further show using in vitro assays that T and Tbx6 differentially affect transcription with Tbx6 activating expression tenfold higher than T, that T and Tbx6 can compete at target gene enhancers, and that this competition requires a functional DNA binding domain. Next, we addressed whether T and Tbx6 can compete in vivo. First, we generated embryos that express Tbx6 at greater than wild-type levels embryos and show that these embryos have short tails, resembling the T heterozygous phenotype. Next, using the dominant-negative TWis allele, we show that Tbx6+/− TWis/+ embryos share similarities with embryos homozygous for the Tbx6 hypomorphic allele rib-vertebrae, specifically fusions of several ribs and malformation of some vertebrae. Finally, we tested whether Tbx6 can functionally replace T using a knockin approach, which resulted in severe T null-like phenotypes in chimeric embryos generated with ES cells heterozygous for a Tbx6 knockin at the T locus. Altogether, our results of differences in affinity for DNA binding sites and transcriptional activity for T and Tbx6 provide a potential mechanism for the failure of Tbx6 to functionally replace T and possible competition phenotypes in vivo. Summary: Mouse Tbx6 fails to compensate for heterozygous loss of T; instead ectopic Tbx6 in the T expression-domain in knockin embryos generates T null-like phenotypes suggestive of competition.
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Affiliation(s)
- Amy K Wehn
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Deborah R Farkas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Carly E Sedlock
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Dibya Subedi
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Deborah L Chapman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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13
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Isoform-specific promotion of breast cancer tumorigenicity by TBX3 involves induction of angiogenesis. J Transl Med 2020; 100:400-413. [PMID: 31570773 PMCID: PMC7044113 DOI: 10.1038/s41374-019-0326-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/13/2019] [Accepted: 09/03/2019] [Indexed: 12/15/2022] Open
Abstract
TBX3 is a member of the highly conserved family of T-box transcription factors involved in embryogenesis, organogenesis and tumor progression. While the functional role of TBX3 in tumorigenesis has been widely studied, less is known about the specific functions of the different isoforms (TBX3iso1 and TBX3iso2) which differ in their DNA-binding domain. We therefore sought to investigate the functional consequence of this highly conserved splice event as it relates to TBX3-induced tumorigenesis. By utilizing a nude mouse xenograft model, we have identified differential tumorigenic potential between TBX3 isoforms, with TBX3iso1 overexpression more commonly associated with invasive carcinoma and high tumor vascularity. Transcriptional analysis of signaling pathways altered by TBX3iso1 and TBX3iso2 overexpression revealed significant differences in angiogenesis-related genes. Importantly, osteopontin (OPN), a cancer-associated secreted phosphoprotein, was significantly up-regulated with TBX3iso1 (but not TBX3iso2) overexpression. This pattern was observed across three non/weakly-tumorigenic breast cancer cell lines (21PT, 21NT, and MCF7). Up-regulation of OPN in TBX3iso1 overexpressing cells was associated with induction of hyaluronan synthase 2 (HAS2) expression and increased retention of hyaluronan in pericellular matrices. These transcriptional changes were accompanied by the ability to induce endothelial cell vascular channel formation by conditioned media in vitro, which could be inhibited through addition of an OPN neutralizing antibody. Within the TCGA breast cancer cohort, we identified an 8.1-fold higher TBX3iso1 to TBX3iso2 transcript ratio in tumors relative to control, and this ratio was positively associated with high-tumor grade and an aggressive molecular subtype. Collectively, the described changes involving TBX3iso1-dependent promotion of angiogenesis may thus serve as an adaptive mechanism within breast cancer cells, potentially explaining differences in tumor formation rates between TBX3 isoforms in vivo. This study is the first of its kind to report significant functional differences between the two TBX3 isoforms, both in vitro and in vivo.
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14
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Eomes and Brachyury control pluripotency exit and germ-layer segregation by changing the chromatin state. Nat Cell Biol 2019; 21:1518-1531. [PMID: 31792383 DOI: 10.1038/s41556-019-0423-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022]
Abstract
The first lineage specification of pluripotent mouse epiblast segregates neuroectoderm (NE) from mesoderm and definitive endoderm (ME) by mechanisms that are not well understood. Here we demonstrate that the induction of ME gene programs critically relies on the T-box transcription factors Eomesodermin (also known as Eomes) and Brachyury, which concomitantly repress pluripotency and NE gene programs. Cells deficient in these T-box transcription factors retain pluripotency and differentiate to NE lineages despite the presence of ME-inducing signals transforming growth factor β (TGF-β)/Nodal and Wnt. Pluripotency and NE gene networks are additionally repressed by ME factors downstream of T-box factor induction, demonstrating a redundancy in program regulation to safeguard mutually exclusive lineage specification. Analyses of chromatin revealed that accessibility of ME enhancers depends on T-box factor binding, whereas NE enhancers are accessible and already activation primed at pluripotency. This asymmetry of the chromatin landscape thus explains the default differentiation of pluripotent cells to NE in the absence of ME induction that depends on activating and repressive functions of Eomes and Brachyury.
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15
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Tian C, Johnson KR. TBX1 is required for normal stria vascularis and semicircular canal development. Dev Biol 2019; 457:91-103. [PMID: 31550482 DOI: 10.1016/j.ydbio.2019.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/12/2019] [Accepted: 09/20/2019] [Indexed: 12/15/2022]
Abstract
Little is known about the role of TBX1 in post-otocyst stages of inner ear development. Here, we report on mice with a missense mutation of Tbx1 that are viable with fully developed but abnormally formed inner ears. Mutant mice are deaf due to an undeveloped stria vascularis and show vestibular dysfunction associated with abnormal semicircular canal formation. We show that TBX1 is expressed in endolymph-producing strial marginal cells and vestibular dark cells of the inner ear and is an upstream regulator of Esrrb, which previously was shown to control the developmental fate of these cells. We also show that TBX1 is expressed in sensory cells of the crista ampullaris, which may relate to the semicircular canal abnormalities observed in mutant mice. Inner ears of mutant embryos have a non-resorbed fusion plate in the posterior semicircular canal and a single ampulla connecting anterior and lateral canals. We hypothesize that the TBX1 missense mutation prevents binding with specific co-regulatory proteins. These findings reveal previously unknown functions of TBX1 during later stages of inner ear development.
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Affiliation(s)
- Cong Tian
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
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16
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Fu C, Li Q, Zou J, Xing C, Luo M, Yin B, Chu J, Yu J, Liu X, Wang HY, Wang RF. JMJD3 regulates CD4 T cell trafficking by targeting actin cytoskeleton regulatory gene Pdlim4. J Clin Invest 2019; 129:4745-4757. [PMID: 31393857 PMCID: PMC6819100 DOI: 10.1172/jci128293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 08/01/2019] [Indexed: 01/23/2023] Open
Abstract
Histone H3K27 demethylase, JMJD3 plays a critical role in gene expression and T-cell differentiation. However, the role and mechanisms of JMJD3 in T cell trafficking remain poorly understood. Here we show that JMJD3 deficiency in CD4+ T cells resulted in an accumulation of T cells in the thymus, and reduction of T cell number in the secondary lymphoid organs. We identified PDLIM4 as a significantly down-regulated target gene in JMJD3-deficient CD4+ T cells by gene profiling and ChIP-seq analyses. We further showed that PDLIM4 functioned as an adaptor protein to interact with S1P1 and filamentous actin (F-actin), thus serving as a key regulator of T cell trafficking. Mechanistically, JMJD3 bound to the promoter and gene body regions of Pdlim4 gene and regulated its expression by interacting with zinc finger transcription factor KLF2. Our findings have identified Pdlim4 as a JMJD3 target gene that affects T-cell trafficking by cooperating with S1P1, and provided insights into the molecular mechanisms by which JMJD3 regulates genes involved in T cell trafficking.
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Affiliation(s)
- Chuntang Fu
- Institute of Bioscience and Technology, Texas A&M University Health Science Center, Houston, Texas, USA
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas, USA
| | - Qingtian Li
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jia Zou
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas, USA
| | - Changsheng Xing
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas, USA
| | - Mei Luo
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas, USA
- Xiangya Hospital, Central South University, Changsha, China
| | - Bingnan Yin
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas, USA
| | - Junjun Chu
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jiaming Yu
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas, USA
| | - Xin Liu
- Institute of Bioscience and Technology, Texas A&M University Health Science Center, Houston, Texas, USA
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas, USA
| | - Helen Y. Wang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas, USA
| | - Rong-Fu Wang
- Institute of Bioscience and Technology, Texas A&M University Health Science Center, Houston, Texas, USA
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas, USA
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17
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Wolski D, Lauer GM. Hepatitis C Virus as a Unique Human Model Disease to Define Differences in the Transcriptional Landscape of T Cells in Acute versus Chronic Infection. Viruses 2019; 11:v11080683. [PMID: 31357397 PMCID: PMC6723887 DOI: 10.3390/v11080683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/21/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022] Open
Abstract
The hepatitis C virus is unique among chronic viral infections in that an acute outcome with complete viral elimination is observed in a minority of infected patients. This unique feature allows direct comparison of successful immune responses with those that fail in the setting of the same human infection. Here we review how this scenario can be used to achieve better understanding of transcriptional regulation of T-cell differentiation. Specifically, we discuss results from a study comparing transcriptional profiles of hepatitis C virus (HCV)-specific CD8 T-cells during early HCV infection between patients that do and do not control and eliminate HCV. Identification of early gene expression differences in key T-cell differentiation molecules as well as clearly distinct transcriptional networks related to cell metabolism and nucleosomal regulation reveal novel insights into the development of exhausted and memory T-cells. With additional transcriptional studies of HCV-specific CD4 and CD8 T-cells in different stages of infection currently underway, we expect HCV infection to become a valuable model disease to study human immunity to viruses.
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Affiliation(s)
- David Wolski
- Liver Center at the Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Georg M Lauer
- Liver Center at the Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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18
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Prier JE, Li J, Gearing LJ, Olshansky M, Sng XYX, Hertzog PJ, Turner SJ. Early T-BET Expression Ensures an Appropriate CD8 + Lineage-Specific Transcriptional Landscape after Influenza A Virus Infection. THE JOURNAL OF IMMUNOLOGY 2019; 203:1044-1054. [PMID: 31227580 DOI: 10.4049/jimmunol.1801431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/31/2019] [Indexed: 01/12/2023]
Abstract
Virus infection triggers large-scale changes in the phenotype and function of naive CD8+ T cells, resulting in the generation of effector and memory T cells that are then critical for immune clearance. The T-BOX family of transcription factors (TFs) are known to play a key role in T cell differentiation, with mice deficient for the TF T-BET (encoded by Tbx21) unable to generate optimal virus-specific effector responses. Although the importance of T-BET in directing optimal virus-specific T cell responses is accepted, the precise timing and molecular mechanism of action remains unclear. Using a mouse model of influenza A virus infection, we demonstrate that although T-BET is not required for early CD8+ T cell activation and cellular division, it is essential for early acquisition of virus-specific CD8+ T cell function and sustained differentiation and expansion. Whole transcriptome analysis at this early time point showed that Tbx21 deficiency resulted in global dysregulation in early programming events with inappropriate lineage-specific signatures apparent with alterations in the potential TF binding landscape. Assessment of histone posttranslational modifications within the Ifng locus demonstrated that Tbx21 -/- CD8+ T cells were unable to activate "poised" enhancer elements compared with wild-type CD8+ T cells, correlating with diminished Ifng transcription. In all, these data support a model whereby T-BET serves to promote appropriate chromatin remodeling at specific gene loci that underpins appropriate CD8+ T cell lineage-specific commitment and differentiation.
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Affiliation(s)
- Julia E Prier
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jasmine Li
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Linden J Gearing
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia; and
| | - Moshe Olshansky
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Xavier Y X Sng
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Paul J Hertzog
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia; and
| | - Stephen J Turner
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia; .,Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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19
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Pawlak M, Kedzierska KZ, Migdal M, Karim AN, Ramilowski JA, Bugajski L, Hashimoto K, Marconi A, Piwocka K, Carninci P, Winata CL. Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development. Genome Res 2019; 29:506-519. [PMID: 30760547 PMCID: PMC6396412 DOI: 10.1101/gr.244491.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/09/2019] [Indexed: 12/19/2022]
Abstract
Organogenesis involves dynamic regulation of gene transcription and complex multipathway interactions. Despite our knowledge of key factors regulating various steps of heart morphogenesis, considerable challenges in understanding its mechanism still exist because little is known about their downstream targets and interactive regulatory network. To better understand transcriptional regulatory mechanism driving heart development and the consequences of its disruption in vivo, we performed time-series analyses of the transcriptome and genome-wide chromatin accessibility in isolated cardiomyocytes (CMs) from wild-type zebrafish embryos at developmental stages corresponding to heart tube morphogenesis, looping, and maturation. We identified genetic regulatory modules driving crucial events of heart development that contained key cardiac TFs and are associated with open chromatin regions enriched for DNA sequence motifs belonging to the family of the corresponding TFs. Loss of function of cardiac TFs Gata5, Tbx5a, and Hand2 affected the cardiac regulatory networks and caused global changes in chromatin accessibility profile, indicating their role in heart development. Among regions with differential chromatin accessibility in mutants were highly conserved noncoding elements that represent putative enhancers driving heart development. The most prominent gene expression changes, which correlated with chromatin accessibility modifications within their proximal promoter regions, occurred between heart tube morphogenesis and looping, and were associated with metabolic shift and hematopoietic/cardiac fate switch during CM maturation. Our results revealed the dynamic regulatory landscape throughout heart development and identified interactive molecular networks driving key events of heart morphogenesis.
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Affiliation(s)
- Michal Pawlak
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Katarzyna Z Kedzierska
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Maciej Migdal
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Abu Nahia Karim
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | | | - Lukasz Bugajski
- Nencki Institute of Experimental Biology, Laboratory of Cytometry, 02-093 Warsaw, Poland
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Aleksandra Marconi
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Katarzyna Piwocka
- Nencki Institute of Experimental Biology, Laboratory of Cytometry, 02-093 Warsaw, Poland
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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20
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Moore-Morris T, van Vliet PP, Andelfinger G, Puceat M. Role of Epigenetics in Cardiac Development and Congenital Diseases. Physiol Rev 2019; 98:2453-2475. [PMID: 30156497 DOI: 10.1152/physrev.00048.2017] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The heart is the first organ to be functional in the fetus. Heart formation is a complex morphogenetic process regulated by both genetic and epigenetic mechanisms. Congenital heart diseases (CHD) are the most prominent congenital diseases. Genetics is not sufficient to explain these diseases or the impact of them on patients. Epigenetics is more and more emerging as a basis for cardiac malformations. This review brings the essential knowledge on cardiac biology of development. It further provides a broad background on epigenetics with a focus on three-dimensional conformation of chromatin. Then, we summarize the current knowledge of the impact of epigenetics on cardiac cell fate decision. We further provide an update on the epigenetic anomalies in the genesis of CHD.
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Affiliation(s)
- Thomas Moore-Morris
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Patrick Piet van Vliet
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Gregor Andelfinger
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Michel Puceat
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
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21
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Khalil A, Dekmak B, Boulos F, Kantrowitz J, Spira A, Fujimoto J, Kadara H, El-Hachem N, Nemer G. Transcriptomic Alterations in Lung Adenocarcinoma Unveil New Mechanisms Targeted by the TBX2 Subfamily of Tumor Suppressor Genes. Front Oncol 2018; 8:482. [PMID: 30425966 PMCID: PMC6218583 DOI: 10.3389/fonc.2018.00482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
T-box (TBX) transcription factors are evolutionary conserved genes and master transcriptional regulators. In mammals, TBX2 subfamily (TBX2, TBX3, TBX4, and TBX5) genes are expressed in the developing lung bud and tracheae. Our group previously showed that the expression of TBX2 subfamily was significantly high in human normal lungs, but markedly suppressed in lung adenocarcinoma (LUAD). To further elucidate their role in LUAD pathogenesis, we first confirmed abundant expression of protein products of the four members by immunostaining in adult human normal lung tissues. We also found overall suppressed expression of these genes and their corresponding proteins in a panel of human LUAD cell lines. Transient over-expression of each of the genes in human (NCI-H1299), and mouse (MDA-F471) derived lung cancer cells was found to significantly inhibit growth and proliferation as well as induce apoptosis. Genome-wide transcriptomic analyses on NCI-H1299 cells, overexpressing TBX2 gene subfamily, unraveled novel regulatory pathways. These included, among others, inhibition of cell cycle progression but more importantly activation of the histone demethylase pathway. When using a pattern-matching algorithm, we showed that TBX's overexpression mimic molecular signatures from azacitidine treated NCI-H1299 cells which in turn are inversely correlated to expression profiles of both human and murine lung tumors relative to matched normal lung. In conclusion, we showed that the TBX2 subfamily genes play a critical tumor suppressor role in lung cancer pathogenesis through regulating its methylating pattern, making them putative candidates for epigenetic therapy in LUAD.
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Affiliation(s)
- Athar Khalil
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Batoul Dekmak
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Fouad Boulos
- Department of Pathology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Jake Kantrowitz
- Section of Computational Biomedicine, Boston University, Boston, MA, United States
| | - Avrum Spira
- Section of Computational Biomedicine, Boston University, Boston, MA, United States
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Humam Kadara
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Division of Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nehme El-Hachem
- Faculty of Medicine and Genome Innovation Centre, McGill University, Montreal, QC, Canada
| | - Georges Nemer
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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22
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Sessa A, Ciabatti E, Drechsel D, Massimino L, Colasante G, Giannelli S, Satoh T, Akira S, Guillemot F, Broccoli V. The Tbr2 Molecular Network Controls Cortical Neuronal Differentiation Through Complementary Genetic and Epigenetic Pathways. Cereb Cortex 2018; 27:3378-3396. [PMID: 27600842 DOI: 10.1093/cercor/bhw270] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 08/04/2016] [Indexed: 01/21/2023] Open
Abstract
The T-box containing Tbr2 gene encodes for a transcription factor essential for the specification of the intermediate neural progenitors (INPs) originating the excitatory neurons of the cerebral cortex. However, its overall mechanism of action, direct target genes and cofactors remain unknown. Herein, we carried out global gene expression profiling combined with genome-wide binding site identification to determine the molecular pathways regulated by TBR2 in INPs. This analysis led to the identification of novel protein-protein interactions that control multiple features of INPs including cell-type identity, morphology, proliferation and migration dynamics. In particular, NEUROG2 and JMJD3 were found to associate with TBR2 revealing unexplored TBR2-dependent mechanisms. These interactions can explain, at least in part, the role of this transcription factor in the implementation of the molecular program controlling developmental milestones during corticogenesis. These data identify TBR2 as a major determinant of the INP-specific traits by regulating both genetic and epigenetic pathways.
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Affiliation(s)
- Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute , 20132 Milan, Italy
| | - Ernesto Ciabatti
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute , 20132 Milan, Italy
| | - Daniela Drechsel
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway ,LondonNW7 1AA, UK
| | - Luca Massimino
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute , 20132 Milan, Italy
| | - Gaia Colasante
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute , 20132 Milan, Italy
| | - Serena Giannelli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute , 20132 Milan, Italy
| | - Takashi Satoh
- Laboratory of Host Defense, Osaka University, Osaka565-0871, Japan
| | - Shizuo Akira
- Laboratory of Host Defense, Osaka University, Osaka565-0871, Japan
| | - Francois Guillemot
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway ,LondonNW7 1AA, UK
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy.,CNR Institute of Neuroscience, 20129 Milan, Italy
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23
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Zhang J, Marotel M, Fauteux-Daniel S, Mathieu AL, Viel S, Marçais A, Walzer T. T-bet and Eomes govern differentiation and function of mouse and human NK cells and ILC1. Eur J Immunol 2018; 48:738-750. [PMID: 29424438 DOI: 10.1002/eji.201747299] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/14/2017] [Accepted: 02/06/2018] [Indexed: 11/08/2022]
Abstract
T-bet and Eomes are T-box transcription factors that drive the differentiation and function of cytotoxic lymphocytes such as NK cells. Their DNA-binding domains are highly similar, suggesting redundant transcriptional activity. However, while these transcription factors have different patterns of expression, the phenotype of loss-of-function mouse models suggests that they play distinct roles in the development of NK cells and other innate lymphoid cells (ILCs). Recent technological advances using reporter mice and conditional knockouts were fundamental in defining the regulation and function of these factors at steady state and during pathological conditions such as various types of cancer or infection. Here, we review these recent developments, focusing on NK cells as prototypical cytotoxic lymphocytes and their development, and also discuss parallels between NK cells and T cells. We also examine the role of T-bet and Eomes in human NK cells and ILC1s. Considering divergent findings on mouse and human ILC1s, we propose that NK cells are defined by coexpression of T-bet and Eomes, while ILC1s express only one of these factors, either T-bet or Eomes, depending on the tissue or the species.
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Affiliation(s)
- Jiang Zhang
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Marie Marotel
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Sébastien Fauteux-Daniel
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Anne-Laure Mathieu
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Sébastien Viel
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Laboratoire d'Immunologie, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, 69495, Pierre-Bénite, France
| | - Antoine Marçais
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Thierry Walzer
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
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24
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Chisolm DA, Weinmann AS. Connections Between Metabolism and Epigenetics in Programming Cellular Differentiation. Annu Rev Immunol 2018; 36:221-246. [PMID: 29328786 DOI: 10.1146/annurev-immunol-042617-053127] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Researchers are intensifying efforts to understand the mechanisms by which changes in metabolic states influence differentiation programs. An emerging objective is to define how fluctuations in metabolites influence the epigenetic states that contribute to differentiation programs. This is because metabolites such as S-adenosylmethionine, acetyl-CoA, α-ketoglutarate, 2-hydroxyglutarate, and butyrate are donors, substrates, cofactors, and antagonists for the activities of epigenetic-modifying complexes and for epigenetic modifications. We discuss this topic from the perspective of specialized CD4+ T cells as well as effector and memory T cell differentiation programs. We also highlight findings from embryonic stem cells that give mechanistic insight into how nutrients processed through pathways such as glycolysis, glutaminolysis, and one-carbon metabolism regulate metabolite levels to influence epigenetic events and discuss similar mechanistic principles in T cells. Finally, we highlight how dysregulated environments, such as the tumor microenvironment, might alter programming events.
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Affiliation(s)
- Danielle A Chisolm
- Department of Microbiology, University of Alabama at Birmingham, Alabama 35294, USA; ,
| | - Amy S Weinmann
- Department of Microbiology, University of Alabama at Birmingham, Alabama 35294, USA; ,
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25
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Beisaw A, Tsaytler P, Koch F, Schmitz SU, Melissari MT, Senft AD, Wittler L, Pennimpede T, Macura K, Herrmann BG, Grote P. BRACHYURY directs histone acetylation to target loci during mesoderm development. EMBO Rep 2017; 19:118-134. [PMID: 29141987 DOI: 10.15252/embr.201744201] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 10/19/2017] [Accepted: 10/25/2017] [Indexed: 12/24/2022] Open
Abstract
T-box transcription factors play essential roles in multiple aspects of vertebrate development. Here, we show that cooperative function of BRACHYURY (T) with histone-modifying enzymes is essential for mouse embryogenesis. A single point mutation (TY88A) results in decreased histone 3 lysine 27 acetylation (H3K27ac) at T target sites, including the T locus, suggesting that T autoregulates the maintenance of its expression and functions by recruiting permissive chromatin modifications to putative enhancers during mesoderm specification. Our data indicate that T mediates H3K27ac recruitment through a physical interaction with p300. In addition, we determine that T plays a prominent role in the specification of hematopoietic and endothelial cell types. Hematopoietic and endothelial gene expression programs are disrupted in TY88A mutant embryos, leading to a defect in the differentiation of hematopoietic progenitors. We show that this role of T is mediated, at least in part, through activation of a distal Lmo2 enhancer.
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Affiliation(s)
- Arica Beisaw
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany.,Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Pavel Tsaytler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Frederic Koch
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sandra U Schmitz
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maria-Theodora Melissari
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anna D Senft
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tracie Pennimpede
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Karol Macura
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical Genetics, Charité-University Medicine Berlin Campus Benjamin Franklin, Berlin, Germany
| | - Phillip Grote
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany .,Institute of Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University, Frankfurt am Main, Germany
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26
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CCCTC-Binding Factor Translates Interleukin 2- and α-Ketoglutarate-Sensitive Metabolic Changes in T Cells into Context-Dependent Gene Programs. Immunity 2017; 47:251-267.e7. [PMID: 28813658 DOI: 10.1016/j.immuni.2017.07.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/21/2017] [Accepted: 07/20/2017] [Indexed: 01/11/2023]
Abstract
Despite considerable research connecting cellular metabolism with differentiation decisions, the underlying mechanisms that translate metabolite-sensitive activities into unique gene programs are still unclear. We found that aspects of the interleukin-2 (IL-2)-sensitive effector gene program in CD4+ and CD8+ T cells in type 1 conditions (Th1) were regulated by glutamine and alpha-ketoglutarate (αKG)-induced events, in part through changes in DNA and histone methylation states. We further identified a mechanism by which IL-2- and αKG-sensitive metabolic changes regulated the association of CCCTC-binding factor (CTCF) with select genomic sites. αKG-sensitive CTCF sites were often associated with loci containing IL-2- and αKG-sensitive genome organization patterns and gene expression in T cells. IL-2- and αKG-sensitive CTCF sites in T cells were also associated with genes from developmental pathways that had αKG-sensitive expression in embryonic stem cells. The data collectively support a mechanism wherein CTCF serves to translate αKG-sensitive metabolic changes into context-dependent differentiation gene programs.
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27
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Zhou Y, Zheng L, Li F, Wan M, Fan Y, Zhou X, Du W, Pi C, Cui D, Zhang B, Sun J, Zhou X. Bivalent Histone Codes on WNT5A during Odontogenic Differentiation. J Dent Res 2017; 97:99-107. [PMID: 28880717 DOI: 10.1177/0022034517728910] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Lineage-committed differentiation is an essential biological program during odontogenesis, which is tightly regulated by lineage-specific genes. Some of these genes are modified by colocalization of H3K4me3 and H3K27me3 marks at promoter regions in progenitors. These modifications, named "bivalent domains," maintain genes in a poised state and then resolve for later activation or repression during differentiation. Wnt5a has been reported to promote odontogenic differentiation in dental mesenchyme. However, relatively little is known about the epigenetic modulations on Wnt5a activation during tooth development. Here, we investigated the spatiotemporal patterns of H3K4me3 and H3K27me3 marks in developing mouse molars. Associated H3K4me3 methylases (mixed-lineage leukemia [MLL] complex) and H3K27me3 demethylases (JMJD3 and UTX) were dynamically expressed between early and late bell stage of human tooth germs and in cultured human dental papilla cells (hDPCs) during odontogenic induction. Poised WNT5A gene was marked by bivalent domains containing repressive marks (H3K27me3) and active marks (H3K4me3) on promoters. The bivalent domains tended to resolve during inducted differentiation, with removal of the H3K27me3 mark in a JMJD3-dependent manner. When JMJD3 was knocked down in cultured hDPCs, odontogenic differentiation was suppressed. The depletion of JMJD3 epigenetically repressed WNT5A activation by increased H3K27me3 marks. In addition, JMJD3 could physically interact with ASH2L, a component of the MLL complex, to form a coactivator complex, cooperatively modulating H3K4me3 marks on WNT5A promoters. Overall, our study reveals that transcription activities of WNT5A were epigenetically regulated by the negotiated balance between H3K27me3 and H3K4me3 marks and tightly mediated by JMJD3 and MLL coactivator complex, ultimately modulating odontogenic commitment during dental mesenchymal cell differentiation.
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Affiliation(s)
- Y Zhou
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - L Zheng
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - F Li
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - M Wan
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Y Fan
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - X Zhou
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - W Du
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - C Pi
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - D Cui
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - B Zhang
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - J Sun
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - X Zhou
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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28
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Northrup D, Yagi R, Cui K, Proctor WR, Wang C, Placek K, Pohl LR, Wang R, Ge K, Zhu J, Zhao K. Histone demethylases UTX and JMJD3 are required for NKT cell development in mice. Cell Biosci 2017; 7:25. [PMID: 28529687 PMCID: PMC5436453 DOI: 10.1186/s13578-017-0152-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 05/02/2017] [Indexed: 02/06/2023] Open
Abstract
Background Natural killer (NK)T cells and conventional T cells share phenotypic characteristic however they differ in transcription factor requirements and functional properties. The role of histone modifying enzymes in conventional T cell development has been extensively studied, little is known about the function of enzymes regulating histone methylation in NKT cells. Results We show that conditional deletion of histone demethylases UTX and JMJD3 by CD4-Cre leads to near complete loss of liver NKT cells, while conventional T cells are less affected. Loss of NKT cells is cell intrinsic and not due to an insufficient selection environment. The absence of NKT cells in UTX/JMJD3-deficient mice protects mice from concanavalin A‐induced liver injury, a model of NKT‐mediated hepatitis. GO‐analysis of RNA-seq data indicates that cell cycle genes are downregulated in UTX/JMJD3-deleted NKT progenitors, and suggest that failed expansion may account for some of the cellular deficiency. The phenotype appears to be demethylase‐dependent, because UTY, a homolog of UTX that lacks catalytic function, is not sufficient to restore their development and removal of H3K27me3 by deletion of EZH2 partially rescues the defect. Conclusions NKT cell development and gene expression is sensitive to proper regulation of H3K27 methylation. The H3K27me3 demethylase enzymes, in particular UTX, promote NKT cell development, and are required for effective NKT function. Electronic supplementary material The online version of this article (doi:10.1186/s13578-017-0152-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Northrup
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health (NIH), Bethesda, MD 20892 USA
| | - Ryoji Yagi
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892 USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health (NIH), Bethesda, MD 20892 USA
| | - William R Proctor
- Center of Immunology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892 USA
| | - Chaochen Wang
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892 USA
| | - Katarzyna Placek
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health (NIH), Bethesda, MD 20892 USA
| | - Lance R Pohl
- Center of Immunology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892 USA
| | - Rongfu Wang
- Departments of Pathology and Immunology, Center for Cell and Gene Therapy, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892 USA
| | - Jinfang Zhu
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892 USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health (NIH), Bethesda, MD 20892 USA
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29
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Chornoguz O, Hagan RS, Haile A, Arwood ML, Gamper CJ, Banerjee A, Powell JD. mTORC1 Promotes T-bet Phosphorylation To Regulate Th1 Differentiation. THE JOURNAL OF IMMUNOLOGY 2017; 198:3939-3948. [PMID: 28424242 DOI: 10.4049/jimmunol.1601078] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 03/21/2017] [Indexed: 12/31/2022]
Abstract
CD4+ T cells lacking the mTORC1 activator Rheb fail to secrete IFN-γ under Th1 polarizing conditions. We hypothesized that this phenotype is due to defects in regulation of the canonical Th1 transcription factor T-bet at the level of protein phosphorylation downstream of mTORC1. To test this hypothesis, we employed targeted mass-spectrometry proteomic analysis-multiple reaction monitoring mass spectrometry. We used this method to detect and quantify predicted phosphopeptides derived from T-bet. By analyzing activated murine wild-type and Rheb-deficient CD4+ T cells, as well as murine CD4+ T cells activated in the presence of rapamycin, a pharmacologic inhibitor of mTORC1, we were able to identify six T-bet phosphorylation sites. Five of these are novel, and four sites are consistently dephosphorylated in both Rheb-deficient CD4+ T cells and T cells treated with rapamycin, suggesting mTORC1 signaling controls their phosphorylation. Alanine mutagenesis of each of the six phosphorylation sites was tested for the ability to impair IFN-γ expression. Single phosphorylation site mutants still support induction of IFN-γ expression; however, simultaneous mutation of three of the mTORC1-dependent sites results in significantly reduced IFN-γ expression. The reduced activity of the triple mutant T-bet is associated with its failure to recruit chromatin remodeling complexes to the Ifng gene promoter. These results establish a novel mechanism by which mTORC1 regulates Th1 differentiation, through control of T-bet phosphorylation.
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Affiliation(s)
- Olesya Chornoguz
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, MD 21287.,Janssen Research and Development, Department of Biologics Research, Spring House, PA 19477
| | - Robert S Hagan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, MD 21287.,Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine, University of North Carolina, Chapel Hill, NC 27599
| | - Azeb Haile
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, MD 21287
| | - Matthew L Arwood
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, MD 21287
| | - Christopher J Gamper
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, MD 21287
| | - Arnob Banerjee
- Program in Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201; and.,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Jonathan D Powell
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287; .,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, MD 21287
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30
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31
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Yang Z, Zhang Q, Lu Q, Jia Z, Chen P, Ma K, Wang W, Zhou C. ISL-1 promotes pancreatic islet cell proliferation by forming an ISL-1/Set7/9/PDX-1 complex. Cell Cycle 2016; 14:3820-9. [PMID: 26176407 PMCID: PMC4825718 DOI: 10.1080/15384101.2015.1069926] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Islet-1 (ISL-1), a LIM-homeodomain transcription factor, has been recently found to be essential for promoting postnatal pancreatic islet proliferation. However, the detailed mechanism has not yet been elucidated. In the present study, we investigated the mechanism by which ISL-1 promotes β-cell proliferation through regulation of CyclinD1 in HIT-T15 and NIT-1 cells, as well in rat islet mass. Our results provide the evidence that ISL-1 promotes adult pancreatic islet β-cell proliferation by activating CyclinD1 transcription through cooperation with Set7/9 and PDX-1 to form an ISL-1/Set7/9/PDX-1 complex. This complex functions in an ISL-1-dependent manner, with Set7/9 functioning not only as a histone methyltransferase, which increases the histone H3K4 tri-methylation of the CyclinD1 promoter region, but also an adaptor to bridge ISL-1 and PDX-1, while PDX-1 functions as a RNA pol II binding modulator. Furthermore, the formation of the ISL-1/Set7/9/PDX-1 complex is positively associated with insulin-like growth factor-1 treatment in NIT and HIT-T15 cells in vitro, while may be negatively correlated with age in vivo.
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Affiliation(s)
- Zhe Yang
- a Department of Biochemistry and Molecular Biology ; School of Basic Medical Sciences; Key Laboratory of Molecular Cardiovascular Sciences; Ministry of Education of China; Peking University ; Beijing , China
| | - Qiao Zhang
- a Department of Biochemistry and Molecular Biology ; School of Basic Medical Sciences; Key Laboratory of Molecular Cardiovascular Sciences; Ministry of Education of China; Peking University ; Beijing , China.,b Current address: Department of Biochemistry and Molecular Biology ; School of Basic Medical Sciences; Kunming Medical University ; Kunming , China
| | - Qin Lu
- a Department of Biochemistry and Molecular Biology ; School of Basic Medical Sciences; Key Laboratory of Molecular Cardiovascular Sciences; Ministry of Education of China; Peking University ; Beijing , China
| | - Zhuqing Jia
- a Department of Biochemistry and Molecular Biology ; School of Basic Medical Sciences; Key Laboratory of Molecular Cardiovascular Sciences; Ministry of Education of China; Peking University ; Beijing , China
| | - Ping Chen
- a Department of Biochemistry and Molecular Biology ; School of Basic Medical Sciences; Key Laboratory of Molecular Cardiovascular Sciences; Ministry of Education of China; Peking University ; Beijing , China
| | - Kangtao Ma
- a Department of Biochemistry and Molecular Biology ; School of Basic Medical Sciences; Key Laboratory of Molecular Cardiovascular Sciences; Ministry of Education of China; Peking University ; Beijing , China
| | - Weiping Wang
- a Department of Biochemistry and Molecular Biology ; School of Basic Medical Sciences; Key Laboratory of Molecular Cardiovascular Sciences; Ministry of Education of China; Peking University ; Beijing , China
| | - Chunyan Zhou
- a Department of Biochemistry and Molecular Biology ; School of Basic Medical Sciences; Key Laboratory of Molecular Cardiovascular Sciences; Ministry of Education of China; Peking University ; Beijing , China
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32
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Hertweck A, Evans CM, Eskandarpour M, Lau JCH, Oleinika K, Jackson I, Kelly A, Ambrose J, Adamson P, Cousins DJ, Lavender P, Calder VL, Lord GM, Jenner RG. T-bet Activates Th1 Genes through Mediator and the Super Elongation Complex. Cell Rep 2016; 15:2756-70. [PMID: 27292648 PMCID: PMC4920892 DOI: 10.1016/j.celrep.2016.05.054] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 04/21/2016] [Accepted: 05/09/2016] [Indexed: 12/21/2022] Open
Abstract
The transcription factor T-bet directs Th1 cell differentiation, but the molecular mechanisms that underlie this lineage-specific gene regulation are not completely understood. Here, we show that T-bet acts through enhancers to allow the recruitment of Mediator and P-TEFb in the form of the super elongation complex (SEC). Th1 genes are occupied by H3K4me3 and RNA polymerase II in Th2 cells, while T-bet-mediated recruitment of P-TEFb in Th1 cells activates transcriptional elongation. P-TEFb is recruited to both genes and enhancers, where it activates enhancer RNA transcription. P-TEFb inhibition and Mediator and SEC knockdown selectively block activation of T-bet target genes, and P-TEFb inhibition abrogates Th1-associated experimental autoimmune uveitis. T-bet activity is independent of changes in NF-κB RelA and Brd4 binding, with T-bet- and NF-κB-mediated pathways instead converging to allow P-TEFb recruitment. These data provide insight into the mechanism through which lineage-specifying factors promote differentiation of alternative T cell fates.
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Affiliation(s)
- Arnulf Hertweck
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK; Department of Experimental Immunobiology and NIHR Comprehensive Biomedical Research Centre, Guy's and St. Thomas' Hospital and King's College London, SE1 9RT London, UK
| | - Catherine M Evans
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK
| | - Malihe Eskandarpour
- UCL Institute of Ophthalmology, University College London, EC1V 9EL London, UK
| | - Jonathan C H Lau
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK
| | - Kristine Oleinika
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK
| | - Ian Jackson
- Department of Experimental Immunobiology and NIHR Comprehensive Biomedical Research Centre, Guy's and St. Thomas' Hospital and King's College London, SE1 9RT London, UK
| | - Audrey Kelly
- Department of Asthma, Allergy, and Respiratory Science, King's College London, SE1 9RT London, UK
| | - John Ambrose
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK
| | - Peter Adamson
- UCL Institute of Ophthalmology, University College London, EC1V 9EL London, UK
| | - David J Cousins
- Department of Asthma, Allergy, and Respiratory Science, King's College London, SE1 9RT London, UK; Leicester Institute for Lung Health and Department of Infection, Immunity, and Inflammation, NIHR Leicester Respiratory Biomedical Research Unit, University of Leicester, LE3 9QP Leicester, UK
| | - Paul Lavender
- Department of Asthma, Allergy, and Respiratory Science, King's College London, SE1 9RT London, UK
| | - Virginia L Calder
- UCL Institute of Ophthalmology, University College London, EC1V 9EL London, UK
| | - Graham M Lord
- Department of Experimental Immunobiology and NIHR Comprehensive Biomedical Research Centre, Guy's and St. Thomas' Hospital and King's College London, SE1 9RT London, UK.
| | - Richard G Jenner
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK.
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Transcriptional regulator Bhlhe40 works as a cofactor of T-bet in the regulation of IFN-γ production in iNKT cells. Proc Natl Acad Sci U S A 2016; 113:E3394-402. [PMID: 27226296 DOI: 10.1073/pnas.1604178113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Invariant natural killer T (iNKT) cells are a subset of innate-like T cells that act as important mediators of immune responses. In particular, iNKT cells have the ability to immediately produce large amounts of IFN-γ upon activation and thus initiate immune responses in various pathological conditions. However, molecular mechanisms that control IFN-γ production in iNKT cells are not fully understood. Here, we report that basic helix-loop-helix transcription factor family, member e40 (Bhlhe40), is an important regulator for IFN-γ production in iNKT cells. Bhlhe40 is highly expressed in stage 3 thymic iNKT cells and iNKT1 subsets, and the level of Bhlhe40 mRNA expression is correlated with Ifng mRNA expression in the resting state. Although Bhlhe40-deficient mice show normal iNKT cell development, Bhlhe40-deficient iNKT cells show significant impairment of IFN-γ production and antitumor effects. Bhlhe40 alone shows no significant effects on Ifng promoter activities but contributes to enhance T-box transcription factor Tbx21 (T-bet)-mediated Ifng promoter activation. Chromatin immunoprecipitation analysis revealed that Bhlhe40 accumulates in the T-box region of the Ifng locus and contributes to histone H3-lysine 9 acetylation of the Ifng locus, which is impaired without T-bet conditions. These results indicate that Bhlhe40 works as a cofactor of T-bet for enhancing IFN-γ production in iNKT cells.
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Harnessing the plasticity of CD4(+) T cells to treat immune-mediated disease. Nat Rev Immunol 2016; 16:149-63. [PMID: 26875830 DOI: 10.1038/nri.2015.18] [Citation(s) in RCA: 353] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CD4(+) T cells differentiate and acquire distinct functions to combat specific pathogens but can also adapt their functions in response to changing circumstances. Although this phenotypic plasticity can be potentially deleterious, driving immune pathology, it also provides important benefits that have led to its evolutionary preservation. Here, we review CD4(+) T cell plasticity by examining the molecular mechanisms that regulate it - from the extracellular cues that initiate and drive cells towards varying phenotypes, to the cytosolic signalling cascades that decipher these cues and transmit them into the cell and to the nucleus, where these signals imprint specific gene expression programmes. By understanding how this functional flexibility is achieved, we may open doors to new therapeutic approaches that harness this property of T cells.
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Fukuoka N, Harada M, Nishida A, Ito Y, Shiota H, Kataoka T. Eomesodermin promotes interferon-γ expression and binds to multiple conserved noncoding sequences across the Ifng locus in mouse thymoma cell lines. Genes Cells 2016; 21:146-62. [PMID: 26749212 DOI: 10.1111/gtc.12328] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 11/23/2015] [Indexed: 01/03/2023]
Abstract
The T-box transcription factors T-bet and eomesodermin (Eomes) have been shown to regulate the lineage-specific expression of interferon-γ (IFN-γ). However, in contrast to T-bet, the role of Eomes in the expression of IFN-γ remains unclear. In this study, we investigated the Eomes-dependent expression of IFN-γ in the mouse thymoma BW5147 and EL4 cells, which do not express T-bet or Eomes. The ectopic expression of Eomes induced BW5147 and EL4 cells to produce IFN-γ in response to phorbol 12-myristate 13-acetate (PMA) and ionomycin (IM). In BW5147 cells, Eomes augmented luciferase activity driven by the Ifng promoter encoding from -2500 to +113 bp; however, it was not increased by a stimulation with PMA and IM. A chromatin immunoprecipitation assay showed that Eomes bound to the Ifng promoter and conserved noncoding sequence (CNS) -22 kb across the Ifng locus with high efficacy in BW5147 cells. Moreover, Eomes increased permissive histone modifications in the Ifng promoter and multiple CNSs. The stimulation with PMA and IM greatly augmented Eomes binding to CNS-54, CNS-34, CNS+19 and CNS+30, which was inhibited by FK506. These results indicated that Eomes bound to the Ifng promoter and multiple CNSs in stimulation-dependent and stimulation-independent manners.
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Affiliation(s)
- Natsuki Fukuoka
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Misuzu Harada
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Ai Nishida
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Yuko Ito
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Hideki Shiota
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Takao Kataoka
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.,Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
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Kofent J, Zhang J, Spagnoli FM. The histone methyltransferase Setd7 promotes pancreatic progenitor identity. Development 2016; 143:3573-3581. [DOI: 10.1242/dev.136226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 08/08/2016] [Indexed: 11/20/2022]
Abstract
Cell fate specification depends on transcriptional activation driven by lineage-specific transcription factors as well as changes in chromatin organization. To date, the interplay between transcription factors and chromatin modifiers during development is not well understood. We focus here on the initiation of the pancreatic program from multipotent endodermal progenitors. Transcription factors that play key roles in regulating pancreatic progenitor state have been identified, but the chromatin regulators that help establishing and maintaining pancreatic fate are less well known. Using a comparative approach, we identify a critical role for the histone methyltransferase Setd7 in establishing pancreatic cell identity. We show that Setd7 is expressed in the prospective pancreatic endoderm of Xenopus and mouse embryos prior to Pdx1 induction. Importantly, we demonstrate that setd7 is sufficient and required for pancreatic cell fate specification in Xenopus. Functional and biochemical approaches in Xenopus and mouse endoderm support that Setd7 modulates methylation marks at pancreatic regulatory regions, possibly through interaction with the transcription factor Foxa2. Together, these results demonstrate that Setd7 acts as a central component of the transcription complex initiating the pancreatic program.
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Affiliation(s)
- Julia Kofent
- Lab. of Molecular and Cellular Basis of Embryonic Development, Max-Delbrück Center for Molecular Medicine, Robert-Roessle strasse 10, Berlin 13125, Germany
| | - Juan Zhang
- Lab. of Molecular and Cellular Basis of Embryonic Development, Max-Delbrück Center for Molecular Medicine, Robert-Roessle strasse 10, Berlin 13125, Germany
| | - Francesca M. Spagnoli
- Lab. of Molecular and Cellular Basis of Embryonic Development, Max-Delbrück Center for Molecular Medicine, Robert-Roessle strasse 10, Berlin 13125, Germany
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Fischer K, Pflugfelder GO. Putative Breast Cancer Driver Mutations in TBX3 Cause Impaired Transcriptional Repression. Front Oncol 2015; 5:244. [PMID: 26579496 PMCID: PMC4625211 DOI: 10.3389/fonc.2015.00244] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 10/14/2015] [Indexed: 12/17/2022] Open
Abstract
The closely related T-box transcription factors TBX2 and TBX3 are frequently overexpressed in melanoma and various types of human cancers, in particular, breast cancer. The overexpression of TBX2 and TBX3 can have several cellular effects, among them suppression of senescence, promotion of epithelial-mesenchymal transition, and invasive cell motility. In contrast, loss of function of TBX3 and most other human T-box genes causes developmental haploinsufficiency syndromes. Stephens and colleagues (1), by exome sequencing of breast tumor samples, identified five different mutations in TBX3, all affecting the DNA-binding T-domain. One in-frame deletion of a single amino acid, p.N212delN, was observed twice. Due to the clustering of these mutations to the T-domain and for statistical reasons, TBX3 was inferred to be a driver gene in breast cancer. Since mutations in the T-domain generally cause loss of function and because the tumorigenic action of TBX3 has generally been attributed to overexpression, we determined whether the putative driver mutations had loss- or gain-of-function properties. We tested two in-frame deletions, one missense, and one frameshift mutant protein for DNA-binding in vitro, and for target gene repression in cell culture. In addition, we performed an in silico analysis of somatic TBX mutations in breast cancer, collected in The Cancer Genome Atlas (TCGA). Both the experimental and the in silico analysis indicate that the observed mutations predominantly cause loss of TBX3 function.
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Beckervordersandforth R, Zhang CL, Lie DC. Transcription-Factor-Dependent Control of Adult Hippocampal Neurogenesis. Cold Spring Harb Perspect Biol 2015; 7:a018879. [PMID: 26430216 DOI: 10.1101/cshperspect.a018879] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Adult-generated dentate granule neurons have emerged as major contributors to hippocampal plasticity. New neurons are generated from neural stem cells through a complex sequence of proliferation, differentiation, and maturation steps. Development of the new neuron is dependent on the precise temporal activity of transcription factors, which coordinate the expression of stage-specific genetic programs. Here, we review current knowledge in transcription factor-mediated regulation of mammalian neural stem cells and neurogenesis and will discuss potential mechanisms of how transcription factor networks, on one hand, allow for precise execution of the developmental sequence and, on the other hand, allow for adaptation of the rate and timing of adult neurogenesis in response to complex stimuli. Understanding transcription factor-mediated control of neuronal development will provide new insights into the mechanisms underlying neurogenesis-dependent plasticity in health and disease.
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Affiliation(s)
- Ruth Beckervordersandforth
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Chun-Li Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Dieter Chichung Lie
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
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Hough KP, Chisolm DA, Weinmann AS. Transcriptional regulation of T cell metabolism. Mol Immunol 2015; 68:520-6. [PMID: 26298576 DOI: 10.1016/j.molimm.2015.07.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/15/2015] [Accepted: 07/29/2015] [Indexed: 11/19/2022]
Abstract
T cells express specific metabolic programs to promote diverse cellular differentiation states. The activation of naïve T cells upregulates the expression of genes encoding components of the glycolysis, glutaminolysis, and lipid biosynthesis pathways to promote robust proliferation and effector T cell activity. In contrast, memory T cells downregulate these pathways and predominantly rely on catabolic pathways for long-term survival. Dynamic changes in the expression of the genes encoding components of metabolic pathways in part define which metabolic programs are utilized in diverse T cell states. The current data suggest that key transcription factors involved in T cell specialization decisions, including T-bet, Bcl-6, HIF1, IRF4 and Myc, link the selective programming of cellular metabolism with fate decisions. In this review, we will highlight the transcriptional regulatory events that define metabolic pathways involved in effector and memory T cell differentiation.
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Affiliation(s)
- Kenneth P Hough
- Department of Microbiology, University of Alabama at Birmingham, USA
| | | | - Amy S Weinmann
- Department of Microbiology, University of Alabama at Birmingham, USA.
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Kang SC, Kim SK, Chai JC, Kim SH, Won KJ, Lee YS, Jung KH, Chai YG. Transcriptomic Profiling and H3K27me3 Distribution Reveal Both Demethylase-Dependent and Independent Regulation of Developmental Gene Transcription in Cell Differentiation. PLoS One 2015; 10:e0135276. [PMID: 26263556 PMCID: PMC4532468 DOI: 10.1371/journal.pone.0135276] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 07/21/2015] [Indexed: 12/19/2022] Open
Abstract
The removal of histone H3 trimethylation at lysine residue 27 (H3K27me3) plays a critical role in the transcriptional initiation of developmental genes. The H3K27me3-specific KDM6 demethylases JMJD3 and UTX are responsible for the transcriptional initiation of various developmental genes, but some genes are expressed in a KDM6 demethylase-independent manner. To address the role of H3K27me3 in the retinoic acid (RA)-induced differentiation of the human carcinoma NCCIT cell line, we inhibited JMJD3 and UTX using the H3K27me3 demethylase inhibitor GSK-J4. The commitment of JMJD3/UTX-inhibited cells to a specific fate was delayed, and transcriptome profiling also revealed the differential expression of genes related to cell fate specification in demethylase-inactivated cells; the expression levels of RA metabolism and HOX family genes significantly decreased. We observed a weak correlation between H3K27me3 enrichment and transcriptional repression in the control and JMJD/UTX-inhibited cells, except for a few sets of developmental genes that are indispensable for cell fate specification. Taken together, these results provide the H3K27me3 landscape of a differentiating cell line and suggest that both demethylase-dependent and demethylase-independent transcriptional regulation play a role in early differentiation and developmental gene expression activated by H3K27me3 demethylation.
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Affiliation(s)
- Sung Chul Kang
- Department of Nanobiotechnology, Hanyang University, Seoul, Republic of Korea
| | - Se Kye Kim
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
| | - Jin Choul Chai
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
| | - Sun Hwa Kim
- Department of Nanobiotechnology, Hanyang University, Seoul, Republic of Korea
| | - Kyoung-Jae Won
- Institute of Diabetes, Obesity, and Metabolism, Genetics Department, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
| | - Young Seek Lee
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
| | - Kyoung Hwa Jung
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
- * E-mail: (YG); (KH)
| | - Young Gyu Chai
- Department of Nanobiotechnology, Hanyang University, Seoul, Republic of Korea
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
- * E-mail: (YG); (KH)
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41
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Burchfield JS, Li Q, Wang HY, Wang RF. JMJD3 as an epigenetic regulator in development and disease. Int J Biochem Cell Biol 2015; 67:148-57. [PMID: 26193001 DOI: 10.1016/j.biocel.2015.07.006] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/13/2015] [Accepted: 07/15/2015] [Indexed: 02/06/2023]
Abstract
Gene expression is epigenetically regulated through DNA methylation and covalent chromatin modifications, such as acetylation, phosphorylation, ubiquitination, sumoylation, and methylation of histones. Histone methylation state is dynamically regulated by different groups of histone methyltransferases and demethylases. The trimethylation of histone 3 (H3K4) at lysine 4 is usually associated with the activation of gene expression, whereas trimethylation of histone 3 at lysine 27 (H3K27) is associated with the repression of gene expression. The polycomb repressive complex contains the H3K27 methyltransferase Ezh2 and controls dimethylation and trimethylation of H3K27 (H3K27me2/3). The Jumonji domain containing-3 (Jmjd3, KDM6B) and ubiquitously transcribed X-chromosome tetratricopeptide repeat protein (UTX, KDM6A) have been identified as H3K27 demethylases that catalyze the demethylation of H3K27me2/3. The role and mechanisms of both JMJD3 and UTX have been extensively studied for their involvement in development, cell plasticity, immune system, neurodegenerative disease, and cancer. In this review, we will focus on recent progresses made on understanding JMJD3 in the regulation of gene expression in development and diseases. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
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Affiliation(s)
- Jana S Burchfield
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Qingtian Li
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Helen Y Wang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Rong-Fu Wang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY 10065, USA.
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42
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Vanyai HK, Thomas T, Voss AK. Mesodermal expression of Moz is necessary for cardiac septum development. Dev Biol 2015; 403:22-9. [DOI: 10.1016/j.ydbio.2015.04.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 10/23/2022]
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Forward Programming of Cardiac Stem Cells by Homogeneous Transduction with MYOCD plus TBX5. PLoS One 2015; 10:e0125384. [PMID: 26047103 PMCID: PMC4457652 DOI: 10.1371/journal.pone.0125384] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/23/2015] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Adult cardiac stem cells (CSCs) express many endogenous cardiogenic transcription factors including members of the Gata, Hand, Mef2, and T-box family. Unlike its DNA-binding targets, Myocardin (Myocd)-a co-activator not only for serum response factor, but also for Gata4 and Tbx5-is not expressed in CSCs. We hypothesised that its absence was a limiting factor for reprogramming. Here, we sought to investigate the susceptibility of adult mouse Sca1+ side population CSCs to reprogramming by supplementing the triad of GATA4, MEF2C, and TBX5 (GMT), and more specifically by testing the effect of the missing co-activator, Myocd. Exogenous factors were expressed via doxycycline-inducible lentiviral vectors in various combinations. High throughput quantitative RT-PCR was used to test expression of 29 cardiac lineage markers two weeks post-induction. GMT induced more than half the analysed cardiac transcripts. However, no protein was detected for the induced sarcomeric genes Actc1, Myh6, and Myl2. Adding MYOCD to GMT affected only slightly the breadth and level of gene induction, but, importantly, triggered expression of all three proteins examined (α-cardiac actin, atrial natriuretic peptide, sarcomeric myosin heavy chains). MYOCD + TBX was the most effective pairwise combination in this system. In clonal derivatives homogenously expressing MYOCD + TBX at high levels, 93% of cardiac transcripts were up-regulated and all five proteins tested were visualized. IN SUMMARY (1) GMT induced cardiac genes in CSCs, but not cardiac proteins under the conditions used. (2) Complementing GMT with MYOCD induced cardiac protein expression, indicating a more complete cardiac differentiation program. (3) Homogeneous transduction with MYOCD + TBX5 facilitated the identification of differentiating cells and the validation of this combinatorial reprogramming strategy. Together, these results highlight the pivotal importance of MYOCD in driving CSCs toward a cardiac muscle fate.
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Christie D, Zhu J. Transcriptional regulatory networks for CD4 T cell differentiation. Curr Top Microbiol Immunol 2015; 381:125-72. [PMID: 24839135 DOI: 10.1007/82_2014_372] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CD4(+) T cells play a central role in controlling the adaptive immune response by secreting cytokines to activate target cells. Naïve CD4(+) T cells differentiate into at least four subsets, Th1Th1 , Th2Th2 , Th17Th17 , and inducible regulatory T cellsregulatory T cells , each with unique functions for pathogen elimination. The differentiation of these subsets is induced in response to cytokine stimulation, which is translated into Stat activation, followed by induction of master regulator transcription factorstranscription factors . In addition to these factors, multiple other transcription factors, both subset specific and shared, are also involved in promoting subset differentiation. This review will focus on the network of transcription factors that control CD4(+) T cell differentiation.
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Affiliation(s)
- Darah Christie
- Molecular and Cellular Immunoregulation Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA,
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Haftmann C, Stittrich AB, Zimmermann J, Fang Z, Hradilkova K, Bardua M, Westendorf K, Heinz GA, Riedel R, Siede J, Lehmann K, Weinberger EE, Zimmel D, Lauer U, Häupl T, Sieper J, Backhaus M, Neumann C, Hoffmann U, Porstner M, Chen W, Grün JR, Baumgrass R, Matz M, Löhning M, Scheffold A, Wittmann J, Chang HD, Rajewsky N, Jäck HM, Radbruch A, Mashreghi MF. miR-148a is upregulated by Twist1 and T-bet and promotes Th1-cell survival by regulating the proapoptotic gene Bim. Eur J Immunol 2015; 45:1192-205. [PMID: 25486906 PMCID: PMC4406154 DOI: 10.1002/eji.201444633] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 11/03/2014] [Accepted: 12/02/2014] [Indexed: 12/31/2022]
Abstract
Repeatedly activated T helper 1 (Th1) cells present during chronic inflammation can efficiently adapt to the inflammatory milieu, for example, by expressing the transcription factor Twist1, which limits the immunopathology caused by Th1 cells. Here, we show that in repeatedly activated murine Th1 cells, Twist1 and T-bet induce expression of microRNA-148a (miR-148a). miR-148a regulates expression of the proapoptotic gene Bim, resulting in a decreased Bim/Bcl2 ratio. Inhibition of miR-148a by antagomirs in repeatedly activated Th1 cells increases the expression of Bim, leading to enhanced apoptosis. Knockdown of Bim expression by siRNA in miR-148a antagomir-treated cells restores viability of the Th1 cells, demonstrating that miR-148a controls survival by regulating Bim expression. Thus, Twist1 and T-bet not only control the differentiation and function of Th1 cells, but also their persistence in chronic inflammation.
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Affiliation(s)
- Claudia Haftmann
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), an institute of the Leibniz AssociationBerlin, Berlin, Germany
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46
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Abstract
Natural killer (NK) cells are innate lymphocytes that survey the environment and protect the host from infected and cancerous cells. As their name implies, NK cells represent an early line of defense during pathogen invasion by directly killing infected cells and secreting inflammatory cytokines. Although the function of NK cells was first described more than four decades ago, the development of this cytotoxic lineage is not well understood. In recent years, we have begun to identify specific transcription factors that control each stage of development and maturation, from ontogeny of the NK cell progenitor to the effector functions of activated NK cells in peripheral organs. This chapter highlights the transcription factors that are unique to NK cells, or shared between NK cells and other hematopoietic cell lineages, but govern the biology of this cytolytic lymphocyte.
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Affiliation(s)
- Joseph C Sun
- Memorial Sloan Kettering Cancer Center, Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, 408 East 69th Street, ZRC-1402, New York, NY, 10065, USA.
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Critical role of histone demethylase Jmjd3 in the regulation of CD4+ T-cell differentiation. Nat Commun 2014; 5:5780. [PMID: 25531312 PMCID: PMC4274750 DOI: 10.1038/ncomms6780] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 11/06/2014] [Indexed: 02/06/2023] Open
Abstract
Epigenetic factors have been implicated in the regulation of CD4+ T cell differentiation. Jmjd3 plays a role in many biological processes, but its in vivo function in T cell differentiation remains unknown. Here, we report that Jmjd3 ablation promotes CD4+ T cell differentiation into Th2 and Th17 cells in the small intestine and colon, and inhibits T cell differentiation into Th1 cells under different cytokine-polarizing conditions and in a Th1-dependent colitis model. Jmjd3 deficiency also restrains the plasticity of the conversion of Th2, Th17 or Treg cells to Th1 cells. The skewing of T cell differentiation is concomitant with changes in the expression of key transcription factors and cytokines. H3K27me3 and H3K4me3 levels in Jmjd3-deficient cells are correlated with altered gene expression through interactions with specific transcription factors. Our results identify Jmjd3 as an epigenetic factor in T cell differentiation via changes in histone methylation and target gene expression.
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48
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Papaioannou VE. The T-box gene family: emerging roles in development, stem cells and cancer. Development 2014; 141:3819-33. [PMID: 25294936 DOI: 10.1242/dev.104471] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The T-box family of transcription factors exhibits widespread involvement throughout development in all metazoans. T-box proteins are characterized by a DNA-binding motif known as the T-domain that binds DNA in a sequence-specific manner. In humans, mutations in many of the genes within the T-box family result in developmental syndromes, and there is increasing evidence to support a role for these factors in certain cancers. In addition, although early studies focused on the role of T-box factors in early embryogenesis, recent studies in mice have uncovered additional roles in unsuspected places, for example in adult stem cell populations. Here, I provide an overview of the key features of T-box transcription factors and highlight their roles and mechanisms of action during various stages of development and in stem/progenitor cell populations.
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Affiliation(s)
- Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
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Vecoli C, Pulignani S, Foffa I, Andreassi MG. Congenital heart disease: the crossroads of genetics, epigenetics and environment. Curr Genomics 2014; 15:390-9. [PMID: 25435801 PMCID: PMC4245698 DOI: 10.2174/1389202915666140716175634] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/24/2014] [Accepted: 07/07/2014] [Indexed: 02/07/2023] Open
Abstract
Congenital heart diseases (CHDs) are recognized as the most common type of birth malformations. Although recent advances in pre- and neonatal diagnosis as well as in surgical procedures have reduced the morbidity and mortality for many CHD, the etiology for CHD remains undefined. In non-syndromic and isolated (without a familial history or a Mendelian inheritance) forms of CHDs, a multifactorial pathogenesis with interplay between inherited and non-inherited causes is recognized. In this paper, we discuss the current knowledge of the potential molecular mechanisms, mediating abnormal cardiac development in non-syndromic and isolated CHD, including mutations in cardiac transcription factors, the role of somatic mutations and epigenetic alterations as well as the influence of gene-environment interactions. In the near future, the advent of high-throughput genomic technologies with the integration of system biology will expand our understanding of isolated, non-syndromic CHDs for their prevention, early diagnosis and therapy.
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Affiliation(s)
| | | | - Ilenia Foffa
- CNR, Institute of Clinical Physiology, Massa, Italy
| | - Maria Grazia Andreassi
- CNR, Institute of Clinical Physiology, Pisa, Italy ; Fondazione Toscana G.Monasterio, Massa, Italy
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Gittenberger-de Groot AC, Calkoen EE, Poelmann RE, Bartelings MM, Jongbloed MRM. Morphogenesis and molecular considerations on congenital cardiac septal defects. Ann Med 2014; 46:640-52. [PMID: 25307363 DOI: 10.3109/07853890.2014.959557] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The primary unseptated heart tube undergoes extensive remodeling including septation at the atrial, atrioventricular, ventricular, and ventriculo-arterial level. Alignment and fusion of the septal components is required to ensure full septation of the heart. Deficiencies lead to septal defects at various levels. Addition of myocardium and mesenchymal tissues from the second heart field (SHF) to the primary heart tube, as well as a population of neural crest cells, provides the necessary cellular players. Surprisingly, the study of the molecular background of these defects does not show a great diversity of responsible transcription factors and downstream gene pathways. Epigenetic modulation and mutations high up in several transcription factor pathways (e.g. NODAL and GATA4) may lead to defects at all levels. Disturbance of modulating pathways, involving primarily the SHF-derived cell populations and the genes expressed therein, results at the arterial pole (e.g. TBX1) in a spectrum of ventricular septal defects located at the level of the outflow tract. At the venous pole (e.g. TBX5), it can explain a variety of atrial septal defects. The various defects can occur as isolated anomalies or within families. In this review developmental, morphological, genetic, as well as epigenetic aspects of septal defects are discussed.
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